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[WIP] Patch for anndata 0.7 (#1132)

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* Fix JSON encoding bug introduced by anndata 0.7

* Add anndata csr and csc classes to allowed matrix proxy inputs
This commit is contained in:
Sidney Bell
2020-01-28 16:12:43 -08:00
committed by GitHub
parent 3dd50e5676
commit a927d733c2
4 changed files with 22 additions and 19 deletions
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server/app/rest_api/rest.py
+1 -1
View File
@@ -45,7 +45,7 @@ class ConfigAPI(Resource):
},
"links": {"about-dataset": current_app.config["ABOUT_DATASET"]},
"parameters": {**current_app.data.get_config_parameters(uid=cxguid, collection=anno_collection)},
"library_versions": {"cellxgene": cellxgene_version, "anndata": anndata_version},
"library_versions": {"cellxgene": cellxgene_version, "anndata": str(anndata_version)},
}
}
server/app/scanpy_engine/matrix_proxy.py
+2
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@@ -38,6 +38,8 @@ class MatrixProxy_anndata_h5py(MatrixProxyView):
"anndata.h5py.h5sparse.backed_csc_matrix",
"anndata.h5py.h5sparse.backed_csr_matrix",
"h5py._hl.dataset.Dataset",
"anndata._core.sparse_dataset.backed_csr_matrix",
"anndata._core.sparse_dataset.backed_csc_matrix",
)
@classmethod
server/app/util/matrix_proxy.py
+2
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@@ -73,6 +73,8 @@ class MatrixProxy(_ArrayProxyBase):
"numpy.ndarray": True,
"scipy.sparse.csc.csc_matrix": True,
"scipy.sparse.csr.csr_matrix": True,
"anndata._core.sparse_dataset.backed_csr_matrix": "MatrixProxy_anndata_h5py",
"anndata._core.sparse_dataset.backed_csc_matrix": "MatrixProxy_anndata_h5py",
}
proxy_registry = None
last_cache_token = None